On 04/21/2016 10:15 AM, Ajay Kurani wrote: > Hi Freesurfer Experts, > > I have used freesurfer smoothed images > (lh.thickness.fsaverage.fwhm15.gii) to perform a cortical thickness > analysis. I used qdec with a surface-based morphometric analysis to > compare two groups. As my discrete fixed factor I used group > membership. As Nuisance factors I used age (years), sex (0/1), > site(1-10) and years of education(years). Not sure what you mean here. Are you treating sex and site as a discrete variables or continuous? Continuous does not make much sense. > I used Threshold min=2, max=5 which I assume refers to a T-stat > threshold. I see an FDR correction which and the Monte Carlo Null-Z > simulation. > > 1) Do I run both monte carlo and fdr or just one after my figure apprears? You would not run them in any combined way if that is what you mean. You would run them independently > > Is the monte-carlo with threshold = 1.3(0.5) similar to a clusterwise > threshold with a fixed p value? It is a clusterwise correction. It uses a monte carlo simulation to determine the chance probability of a cluster of a given size. Other packages use gaussian random field theory to do the same thing (but it makes a lot of assumptions). > Are results valid when just setting the threshold min=2, max=5 but > they are just uncorrected results? what do you mean? you were just talking about cluster correction > > > 2) When running Qdec with no nusiance factors and just a discrete > fixed factor of group membership, my results look almost identical to > AFNI's 3dttest++ output when the tmin=2. However, when I add the > nuisance factors the results between the two softare packages are > different. > > When nuisances covariates are added does Qdec still use a ttest or > switch to some other method? Still uses t-test. Probably the design matrix is changing between the two packages. > > > How is centering assumed between groups for covariances? Is the mean > from each covariate calculated and removed from each group separately > based on group membership or calculated together with all subjects and > removed? No centering is done. You have to do this yourself. > > Does the analysis assume to have pooled or unpooled variance across > the two groups? It pools variance across the groups. > > > 3) For the viewer it displaces a logarithmic scale from what I have > read in other papers. Is there a way to switch this to displace tvalue? Not in qdec. you can run freeview outside of qdec to view the tmaps > > 4) There was a previous post I saw yesterday saying qdec only uses 2 > nuisance covariates and so I wanted to see if this is the case or not > so I can try to understand why my afni and freesurfer results match > with no covariates added but are very different once covariates are added. yes it is. You can also look at the design matrix (Xg.dat) in the output folder and compare that to whatever afni is using > > > Thanks, > Ajay > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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